Diffusion SpecMiCP / ReactMiCP b174f1ddf352

License update before release
b174f1ddf352
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Authored by fabien on Apr 15 2015, 22:11.

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License update before release

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fabien

Apr 15 2015, 22:11

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rSPECMICP94f086f45381: Documentation for the database/species module

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tag: 0.0.3

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fabien committed rSPECMICPb174f1ddf352: License update before release (authored by fabien).Apr 15 2015, 22:11

Changes (170)

				Path
	M			COPYING
	M			cython/specmicp/__init__.py
	M			cython/specmicp/cement_hydration.py
	M			cython/specmicp/constraints.pxd
	M			cython/specmicp/constraints.pyx
	M			cython/specmicp/database.pxd
	M			cython/specmicp/database.pyx
	M			cython/specmicp/init_log.hpp
	M			cython/specmicp/is_solver_successful.hpp
	M			cython/specmicp/logger.pxd
	M			cython/specmicp/logger.pyx
	M			cython/specmicp/set_units.hpp
	M			cython/specmicp/solution.pxd
	M			cython/specmicp/solution.pyx
	M			cython/specmicp/solver.pxd
	M			cython/specmicp/solver.pyx
	M			cython/specmicp/solver_options.pxd
	M			cython/specmicp/units.pxd
	M			examples/reactmicp/saturated_react/carbonation.cpp
	M			examples/reactmicp/saturated_react/carbonationfe.cpp
	M			examples/reactmicp/saturated_react/react_leaching.cpp
	M			src/common.hpp
	M			src/database.hpp
	M			src/database/aqueous_selector.cpp
	M			src/database/aqueous_selector.hpp
	M			src/database/data_container.cpp
	M			src/database/data_container.hpp
	M			src/database/database.cpp
	M			src/database/database.hpp
	M			src/database/errors.hpp
	M			src/database/mineral_selector.cpp
	M			src/database/mineral_selector.hpp
	M			src/database/module.hpp
	M			src/database/oxydo_selector.cpp
	M			src/database/oxydo_selector.hpp
	M			src/database/reader.cpp
	M			src/database/reader.hpp
	M			src/database/selector.cpp
	M			src/database/selector.hpp
	M			src/database/species/aqueous_list.hpp
	M			src/database/species/base_wrapper.cpp
	M			src/database/species/base_wrapper.hpp
	M			src/database/species/component_list.hpp
	M			src/database/species/gas_list.hpp
	M			src/database/species/ionic_parameters.hpp
	M			src/database/species/mineral_list.hpp
	M			src/database/species/sorbed_list.hpp
	M			src/database/species/species.cpp
	M			src/database/species/species.hpp
	M			src/database/switch_basis.cpp
	M			src/database/switch_basis.hpp
	M			src/dfpm/1dtransport/diffusion.cpp
	M			src/dfpm/1dtransport/diffusion.hpp
	M			src/dfpm/1dtransport/diffusion_parameters.hpp
	M			src/dfpm/mesh.hpp
	M			src/dfpm/meshes/axisymmetric_mesh1d.hpp
	M			src/dfpm/meshes/axisymmetric_uniform_mesh1d.hpp
	M			src/dfpm/meshes/generic_mesh1d.hpp
	M			src/dfpm/meshes/mesh1d.hpp
	M			src/dfpm/meshes/mesh1dfwd.hpp
	M			src/dfpm/meshes/uniform_mesh1d.hpp
	M			src/dfpm/types.hpp
	M			src/dfpmsolver/dfpm_program.hpp
	M			src/dfpmsolver/driver.hpp
	M			src/dfpmsolver/driver.inl
	M			src/dfpmsolver/driver_structs.hpp
	M			src/dfpmsolver/parabolic_driver.hpp
	M			src/dfpmsolver/parabolic_driver.inl
	M			src/dfpmsolver/parabolic_program.hpp
	M			src/dfpmsolver/parabolic_structs.hpp
	M			src/micpsolver/estimate_cond_number.hpp
	M			src/micpsolver/micpprog.hpp
	M			src/micpsolver/micpsolver.hpp
	M			src/micpsolver/micpsolver.inl
	M			src/micpsolver/micpsolver_base.hpp
	M			src/micpsolver/micpsolver_base.inl
	M			src/micpsolver/micpsolver_min.hpp
	M			src/micpsolver/micpsolver_min.inl
	M			src/micpsolver/micpsolver_structs.hpp
	M			src/micpsolver/micpsolverold.hpp
	M			src/micpsolver/micpsolverold.inl
	M			src/micpsolver/ncp_function.hpp
	M			src/odeint/butcher_tableau.hpp
	M			src/odeint/odeint_types.hpp
	M			src/odeint/runge_kutta_step.hpp
	M			src/odeint/runge_kutta_step.inl
	M			src/odeint/runge_kutta_step_structs.hpp
	M			src/physics/constants.hpp
	M			src/physics/laws.hpp
	M			src/physics/units.hpp
	M			src/reactmicp.hpp
	M			src/reactmicp/equilibrium_curve/chemistry.cpp
	M			src/reactmicp/equilibrium_curve/chemistry.hpp
	M			src/reactmicp/equilibrium_curve/eqcurve_coupler.cpp
	M			src/reactmicp/equilibrium_curve/eqcurve_coupler.hpp
	M			src/reactmicp/equilibrium_curve/eqcurve_extractor.cpp
	M			src/reactmicp/equilibrium_curve/eqcurve_extractor.hpp
	M			src/reactmicp/equilibrium_curve/eqcurve_solid_transport.cpp
	M			src/reactmicp/equilibrium_curve/eqcurve_solid_transport.hpp
	M			src/reactmicp/solver/reactive_transport_solver.cpp
	M			src/reactmicp/solver/reactive_transport_solver.hpp
	M			src/reactmicp/solver/reactive_transport_solver_structs.hpp
	M			src/reactmicp/solver/runner.cpp
	M			src/reactmicp/solver/runner.hpp
	M			src/reactmicp/solver/staggers_base/chemistry_stagger_base.hpp
	M			src/reactmicp/solver/staggers_base/decl.inl
	M			src/reactmicp/solver/staggers_base/stagger_structs.hpp
	M			src/reactmicp/solver/staggers_base/staggers_base.hpp
	M			src/reactmicp/solver/staggers_base/transport_stagger_base.hpp
	M			src/reactmicp/solver/staggers_base/upscaling_stagger_base.hpp
	M			src/reactmicp/solver/staggers_base/variables_base.hpp
	M			src/reactmicp/solver/timestepper.cpp
	M			src/reactmicp/solver/timestepper.hpp
	M			src/reactmicp/systems/saturated_react/equilibrium_stagger.cpp
	M			src/reactmicp/systems/saturated_react/equilibrium_stagger.hpp
	M			src/reactmicp/systems/saturated_react/init_variables.cpp
	M			src/reactmicp/systems/saturated_react/init_variables.hpp
	M			src/reactmicp/systems/saturated_react/react_solver.cpp
	M			src/reactmicp/systems/saturated_react/react_solver.hpp
	M			src/reactmicp/systems/saturated_react/transport_program.cpp
	M			src/reactmicp/systems/saturated_react/transport_program.hpp
	M			src/reactmicp/systems/saturated_react/transport_stagger.cpp
	M			src/reactmicp/systems/saturated_react/transport_stagger.hpp
	M			src/reactmicp/systems/saturated_react/variables.cpp
	M			src/reactmicp/systems/saturated_react/variables.hpp
	M			src/reactmicp/systems/saturated_react/variablesfwd.hpp
	M			src/specmicp.hpp
	M			src/specmicp/adimensional/adimensional_system.cpp
	M			src/specmicp/adimensional/adimensional_system.hpp
	M			src/specmicp/adimensional/adimensional_system_numbering.hpp
	M			src/specmicp/adimensional/adimensional_system_pcfm.cpp
	M			src/specmicp/adimensional/adimensional_system_pcfm.hpp
	M			src/specmicp/adimensional/adimensional_system_pcfm_structs.hpp
	M			src/specmicp/adimensional/adimensional_system_solution.hpp
	M			src/specmicp/adimensional/adimensional_system_solution_extractor.cpp
	M			src/specmicp/adimensional/adimensional_system_solution_extractor.hpp
	M			src/specmicp/adimensional/adimensional_system_solver.cpp
	M			src/specmicp/adimensional/adimensional_system_solver.hpp
	M			src/specmicp/adimensional/adimensional_system_solver_structs.hpp
	M			src/specmicp/adimensional/adimensional_system_structs.hpp
	M			src/specmicp/adimensional/equilibrium_curve.cpp
	M			src/specmicp/adimensional/equilibrium_curve.hpp
	M			src/specmicp/adimensional_kinetics/kinetic_model.hpp
	M			src/specmicp/adimensional_kinetics/kinetic_system.cpp
	M			src/specmicp/adimensional_kinetics/kinetic_system.hpp
	M			src/specmicp/adimensional_kinetics/kinetic_system_euler_solver.cpp
	M			src/specmicp/adimensional_kinetics/kinetic_system_euler_solver.hpp
	M			src/specmicp/adimensional_kinetics/kinetic_system_solver.cpp
	M			src/specmicp/adimensional_kinetics/kinetic_system_solver.hpp
	M			src/specmicp/adimensional_kinetics/kinetic_system_solver_structs.hpp
	M			src/specmicp/adimensional_kinetics/kinetic_variables.hpp
	M			src/specmicp/problem_solver/dissolver.cpp
	M			src/specmicp/problem_solver/dissolver.hpp
	M			src/specmicp/problem_solver/formulation.hpp
	M			src/utils/io/meshes.hpp
	M			src/utils/io/reactive_transport.hpp
	M			src/utils/io/saturated_react.hpp
	M			src/utils/io/units.hpp
	M			src/utils/log.hpp
	M			src/utils/moving_average.hpp
	M			src/utils/options_handler.hpp
	M			src/utils/perfs_handler.hpp
	M			src/utils/sparse_solvers/sparse_bicgstab.hpp
	M			src/utils/sparse_solvers/sparse_gmres.hpp
	M			src/utils/sparse_solvers/sparse_lu.hpp
	M			src/utils/sparse_solvers/sparse_qr.hpp
	M			src/utils/sparse_solvers/sparse_solver.hpp
	M			src/utils/sparse_solvers/sparse_solver_base.hpp
	M			src/utils/sparse_solvers/sparse_solver_structs.hpp
	M			src/utils/timer.hpp